Variant report

Variant	rs11738876
Chromosome Location	chr5:97654953-97654954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10515275	0.81[GIH][hapmap]
rs11745914	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11957758	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12513398	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12652566	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12654883	0.94[ASN][1000 genomes]
rs13355852	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13359215	0.83[AMR][1000 genomes]
rs1350022	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1378444	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1455429	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1455430	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17165846	0.94[ASN][1000 genomes]
rs17165848	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17165849	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2061115	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2198680	0.82[EUR][1000 genomes]
rs35774032	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4538635	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4559027	0.90[ASN][1000 genomes]
rs60805392	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62366857	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6876270	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6889185	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898721	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921815	0.92[ASN][1000 genomes]
rs961713	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882407	chr5:97553255-97783046	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv882408	chr5:97616089-97836794	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv830419	chr5:97653713-97829079	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11738876	MCTP1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:97646200-97655200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr5:97646400-97655600	Weak transcription	Brain Substantia Nigra	brain
3	chr5:97651200-97656000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:97651200-97656000	Weak transcription	Brain Anterior Caudate	brain
5	chr5:97652600-97655000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:97652600-97655000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:97653400-97657000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:97653600-97655200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:97654200-97655000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:97654600-97655800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:97654800-97656000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr5:97654800-97656000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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